In the year 3999, New York City is in ruins. The mutant known as Cable and his team is counterattacking Apocalypse’s troops. Suddenly, a “temporal storm” appears and Cable’s team is being sucked into the storm. Cable is being informed that due to changes in the past, his present is “realigning itself”. But as soon as “the timestream is realigned, [him] and [his] world will cease to exist”. Cable’s information source replays the changed events in the past.
Bishop has returned to his present in the year 2055 since accomplishing his mission. Although he has stopped the assassination of Senator Kelly, another threat strikes mutants as a form of “genetically-engineered” virus, killing mutants. In this altered present, the X-Men ceased to exist. Bishop demands that Forge send him back to the past.
Bishop arrives back in the 90s. The “plague” had already begun to spread. Bishop rushes off to find the X-Men.
Storm accompanies Jubilee to get her CD player fixed. As the store clerk of the electronics store goes into the back to fix Jubilee’s CD player, the leader of the Friends of Humanity (FoH), Creed, releases the airborne virus into the room, infecting the store clerk. The leader of the FoH accuses Jubilee of carrying the “plague”. Storm distracts the angry crowd and gets Jubilee back to the mansion.
Beast does a full body scan on Jubilee but finds “no signs of infection”. Jean comforts Jubilee, telling her that everyone is looking for a scapegoat to blame for the virus, and “mutants are an easy target”.
Beast sneaks into the hospital to examine the store clerk’s blood sample.
Meanwhile, city officials have begun the quarantine of mutants in an effort to stop the virus from spreading. Storm recognises Creed on the news broadcast from the mall. The X-Men rush to the scene of the riot as reported on the news. They find Bishop. Storm disperses the crowd with rain.
Back in the mansion, Bishop explains what had happened to the changed future. The “plague” was created in a laboratory, and the X-Men had probably died after contracting the virus. Beast returns with his findings from the hospital. Beast predicts that once the virus “combines with mutant DNA” and mutates, it will become deadly.
Creed urges his head scientist to embark on phase two of his plan: to infect mutants, specially Beast at the meeting in Washington DC the following morning, to show the world that “mutants are responsible”. The scientist turns out to be Apocalypse in disguise, with his own agenda: to wipe out mutants and humans with the virus.
At the meeting, Creed firmly stands by his claim that mutants are the cause of the virus. When Beast is called to the stand to give his statement, Creed tries to seize the opportunity to infect Beast. Bishop notices Creed’s actions and lungs forward to stop the latter. A fight breaks out. Creed infected himself with the virus, the public is now inclined to believe that Bishop’s attack infected Creed.
Cyclops orders Bishop’s restraint. In the Blackbird, Beast plays back the recorded session and confirms Bishop’s claims that Creed was carrying a viral weapon.
The X-Men arrive at the FoH headquarters after following Creed. Jean telepathically scans the grounds. Creed had retreated beneath the mansion. There is also a presence of a powerful mutant who counterattacked Jean’s scans. Creed goes to the scientist to beg for a cure, the X-Men hot on his heels. Apocalypse reveals himself, furious that Creed had “led the X-Men to [him]”.
The X-Men prove powerless against Apocalypse so Bishop destroys the virus instead and sets the lab on fire.
Back in 3999, due to the fact that the virus never infected mutants, antibodies that led to the “stabilisation of the mutant genetic code” did not develop. Mutants slowly died out, and Cable’s future ceased to exist. Ironically, Cable has to help Apocalypse spread the “plague” to preserve the future.